1-171090009-C-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The ENST00000653116.1(ENSG00000231424):​n.542+78095G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,684 control chromosomes in the GnomAD database, including 6,963 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.29 ( 6963 hom., cov: 31)

Consequence

ENSG00000231424
ENST00000653116.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0650
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BP6
Variant 1-171090009-C-G is Benign according to our data. Variant chr1-171090009-C-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000231424ENST00000653116.1 linkn.542+78095G>C intron_variant Intron 3 of 3
ENSG00000231424ENST00000664920.1 linkn.681+31741G>C intron_variant Intron 4 of 5
ENSG00000231424ENST00000669750.1 linkn.533+78095G>C intron_variant Intron 3 of 4
ENSG00000231424ENST00000670085.1 linkn.371+78095G>C intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
AF:
0.294
AC:
44518
AN:
151570
Hom.:
6943
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.215
Gnomad AMI
AF:
0.293
Gnomad AMR
AF:
0.371
Gnomad ASJ
AF:
0.289
Gnomad EAS
AF:
0.576
Gnomad SAS
AF:
0.310
Gnomad FIN
AF:
0.305
Gnomad MID
AF:
0.266
Gnomad NFE
AF:
0.300
Gnomad OTH
AF:
0.274
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.294
AC:
44564
AN:
151684
Hom.:
6963
Cov.:
31
AF XY:
0.299
AC XY:
22139
AN XY:
74114
show subpopulations
Gnomad4 AFR
AF:
0.215
Gnomad4 AMR
AF:
0.372
Gnomad4 ASJ
AF:
0.289
Gnomad4 EAS
AF:
0.576
Gnomad4 SAS
AF:
0.309
Gnomad4 FIN
AF:
0.305
Gnomad4 NFE
AF:
0.300
Gnomad4 OTH
AF:
0.276
Alfa
AF:
0.170
Hom.:
359
Bravo
AF:
0.293
Asia WGS
AF:
0.438
AC:
1517
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.89
DANN
Benign
0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1736560; hg19: chr1-171059150; API